Résumé : Ce rapport clôture une collaboration, entreprise courant 97, entre l’Agence Nationale pour la Valorisation de la Recherche (ANVAR), l’Agence Française de Sécurité Sanitaire des Aliments(AFSSA), le Syndicat National des Aquaculteurs Marins (SFAM) et l’Institut Français de Recherche pour l’Exploitation de la Mer (IFREMER). Deux lignées de nodavirus infectant le bar ont été mises en évidence avec une pathogénie variable selon l'âge et les facteurs extérieurs. Ce virus s’est montré d’une résistance exceptionnelle aux facteurs tant physiques que chimiques. Les diagnostics existants ont été adaptés ou réabordés sous un angle différent. Une étude épidémiologique a été réalisée chez les producteurs. La vaccination par peptides synthétiques a permis de sélectionner un peptide potentiellement protecteur et des essais de vaccin par injection des plasmides directement chez le poisson ont été réalisés. La désinfection et l’inactivation du virus ont donné des bons résultats.

Droits : 2002 Ifremer, Afssa, Anvar
http://archimer.ifremer.fr/doc/00167/27874/26120.pdf
http://archimer.ifremer.fr/doc/00167/27874/26121.pdf
http://archimer.ifremer.fr/doc/00167/27874/

Éditeur(s) : HAL CCSD eLife Sciences Publication
Résumé : International audience
Plastids are supported by a wide range of proteins encoded within the nucleus and imported from the cytoplasm. These plastid-targeted proteins may originate from the endosymbiont, the host, or other sources entirely. Here, we identify and characterise 770 plastid-targeted proteins that are conserved across the ochrophytes, a major group of algae including diatoms, pelagophytes and kelps, that possess plastids derived from red algae. We show that the ancestral ochrophyte plastid proteome was an evolutionary chimera, with 25% of its phylogenetically tractable proteins deriving from green algae. We additionally show that functional mixing of host and plastid proteomes, such as through dual targeting, is an ancestral feature of plastid evolution. Finally, we detect a clear phylogenetic signal from one ochrophyte subgroup, the lineage containing pelagophytes and dictyochophytes, in plastid-targeted proteins from another major algal lineage, the haptophytes. This may represent a possible serial endosymbiosis event deep in eukaryotic evolutionary history.
ISSN: 2050-084X

Droits : http://creativecommons.org/licenses/by/
hal-01526828
http://hal.upmc.fr/hal-01526828
http://hal.upmc.fr/hal-01526828/document
http://hal.upmc.fr/hal-01526828/file/e23717-download.pdf
DOI : 10.7554/eLife.23717

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : International audience
To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V. tritonius sp. nov., which is a member of the “Porteresiae” clade.
ISSN: 1664-302X

hal-01546980
http://hal.upmc.fr/hal-01546980
DOI : 10.3389/fmicb.2013.00414

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The number of satellites and sensors devoted to Earth observation has become increasingly elevated, delivering extensive data, especially images. At the same time, the access to such data and the tools needed to process them has considerably improved. In the presence of such data flow, we need automatic image interpretation methods, especially when it comes to the monitoring and prediction of environmental and societal changes in highly dynamic socio-environmental contexts. This could be accomplished via artificial intelligence. The concept described here relies on the induction of classification rules that explicitly take into account structural knowledge, using Aleph, an Inductive Logic Programming (ILP) system, combined with a multi-class classification procedure. This methodology was used to monitor changes in land cover/use of the French Guiana coastline. One hundred and fifty-eight classification rules were induced from 3 diachronic land cover/use maps including 38 classes. These rules were expressed in first order logic language, which makes them easily understandable by non-experts. A 10-fold cross-validation gave significant average values of 84.62%, 99.57% and 77.22% for classification accuracy, specificity and sensitivity, respectively. Our methodology could be beneficial to automatically classify new objects and to facilitate object-based classification procedures.
ISSN: 0098-3004

hal-01369822
https://hal.archives-ouvertes.fr/hal-01369822
https://hal.archives-ouvertes.fr/hal-01369822/document
https://hal.archives-ouvertes.fr/hal-01369822/file/CAGEO-D-13-00538R1_article.pdf
DOI : 10.1016/j.cageo.2014.08.013

Éditeur(s) : HAL CCSD
Résumé : International audience
Direct examinations of blood and serologic tests were used to assess the intensity of the filarial endemicity in Gabon. Both methods revealed that the prevalence of filariasis with microfilaremia (Loa loa and Dipetalonema perstans) is presently very elevated. The areas that are more involved are the forest regions as well as the highest ones (ogoue, Lolo, Ngounie). Women appeared to be suffering from loasis to a lesser extent than men. On the other hand, the prevalence was identical for Dipetalonema perstans. For the gabonese population one can approximately say that 3 out of 5 adults patients have filariasis, two being D. perstans and one L. loa. Consequently these affections represent a major public health problem. Finally one must note that no case of lymphatic filariasis has been identified.
Bull Soc Pathol Exot Filiales

hal-00717069
https://hal.univ-antilles.fr/hal-00717069
PUBMED : 6936082

Éditeur(s) : HAL CCSD
Résumé : International audience
Le nombre de satellites et de capteurs pour la télédétection dédiés à l'observation de la Terre ne cesse d'augmenter, permettant ainsi d'avoir une masse de données importante en particulier en matière d'images. Parallèlement, un effort permanent vise, d'une part, à améliorer l'accès à ces données et, d'autre part, à développer d'avantages d'outils pour les manipuler. De tels efforts sont particulièrement utiles dans des contextes socio-environnementaux très dynamiques spatialement et temporellement, pour lesquels il est nécessaire de suivre et de prédire les événements environnementaux et sociétaux. En revanche, en présence d'un tel flux de données, nous avons besoin de méthodes automatiques d'interprétation d'images. Une solution envisageable pour répondre à ce besoin est de bénéficier des atouts de l'intelligence artificielle pour l'obtention de cartes d'occupation du sol issues d'une classification des régions des images. Afin de contribuer à l'automatisation de la classification, nous proposons une méthode d'induction de règles interprétables par des non-experts et mettant en évidence, explicitement, des connaissances structurelles. Cette méthode s'appuie sur la programmation logique inductive (PLI) et en particulier sur le système inductif ”Aleph”. L'application de la méthode de classification Multi-class Rule Set Intersection (MRSI) permet ensuite de classifier tout nouvel objet au regard des ses caractéristiques intrinsèques et de celles des objets environnants. Nous avons appliqué notre méthodologie à l'étude de la dynamique du littoral de la Guyane Française. Suite à ce travail, nous avons induit 136 règles de classification pour 38 classes d'occupation du sol. Ces règles sont intelligibles et simples à interpréter de par l'utilisation de la logique du premier ordre. Les performances du système ont été évaluées par la validation croisée. En moyenne, la précision, la spécificité et la sensibilité sont, respectivement, égales à 84,62%, 99,57% et 77,22%. Ces résultats quantitatifs montrent une bonne performance de la méthodologie pour la mise à jour automatique de cartes d'occupation du sol et/ou l'assistance aux opérateurs utilisant l'analyse d'image orientée-objet.
11èmes Rencontres des Jeunes Chercheurs en Intelligence Artificielle
Lille, France

hal-01376400
https://hal.archives-ouvertes.fr/hal-01376400
https://hal.archives-ouvertes.fr/hal-01376400/document
https://hal.archives-ouvertes.fr/hal-01376400/file/Bayoudh_RJCIA2013.pdf

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Pituitary adenomas are currently classified by histological, immunocytochemical and numerous ultrastructural characteristics lacking unequivocal prognostic correlations. We investigated the prognostic value of a new clinicopathological classification with grades based on invasion and proliferation. This retrospective multicentric case-control study comprised 410 patients who had surgery for a pituitary tumour with long-term follow-up. Using pituitary magnetic resonance imaging for diagnosis of cavernous or sphenoid sinus invasion, immunocytochemistry, markers of the cell cycle (Ki-67, mitoses) and p53, tumours were classified according to size (micro, macro and giant), type (PRL, GH, FSH/LH, ACTH and TSH) and grade (grade 1a: non-invasive, 1b: non-invasive and proliferative, 2a: invasive, 2b: invasive and proliferative, and 3: metastatic). The association between patient status at 8-year follow-up and age, sex, and classification was evaluated by two multivariate analyses assessing disease- or recurrence/progression-free status. At 8 years after surgery, 195 patients were disease-free (controls) and 215 patients were not (cases). In 125 of the cases the tumours had recurred or progressed. Analyses of disease-free and recurrence/progression-free status revealed the significant prognostic value (p < 0.001; p < 0.05) of age, tumour type, and grade across all tumour types and for each tumour type. Invasive and proliferative tumours (grade 2b) had a poor prognosis with an increased probability of tumour persistence or progression of 25- or 12-fold, respectively, as compared to non-invasive tumours (grade 1a). This new, easy to use clinicopathological classification of pituitary endocrine tumours has demonstrated its prognostic worth by strongly predicting the probability of post-operative complete remission or tumour progression and so could help clinicians choose the best post-operative therapy.
ISSN: 0001-6322

hal-00875723
https://hal.archives-ouvertes.fr/hal-00875723
DOI : 10.1007/s00401-013-1084-y
PUBMED : 23400299

Éditeur(s) : HAL CCSD BRGM
Résumé : National audience
Proceedings 1ère Journée 'Alea Gravitaire'
Orléans, France

hal-00533951
https://hal.archives-ouvertes.fr/hal-00533951